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Biology I Midterm I
Terms in this set (89)
What are the four main classes of large biological molecules?
Proteins, Carbohydrates, Lipids, Nucleic Acids
Which of the four macromolecules is not made up of polymers?
How many water molecules are required to hydrolyze a 10-monomer polymer?
How does your body convert the polymers in food intake into new polymers?
The polymers are first separated with hydrolysis reactions, then joined in new orders/incorporated into other proteins with dehydration synthesis.
Define glycosidic linkage.
Covalent bond formed between a sugar and another molecule
Define starch and describe its structure. (Solubility, function, type of monomer, structure)
Water-soluble polymer of alpha-glucose that is used in plant storage; all alpha-glucose monomers are orientated in the same direction and have (1,4) glycosidic linkages; can be branched or unbranched
What is the general formula for a monosaccharide?
Draw the linear and ring forms of ribose and glucose.
Define cellulose and describe its structure. (Solubility, function, type of monomer, structure)
Water-insoluble polymer of beta-glucose that is used in plant structure; made up of hydrogen-bonded strands of beta-glucose monomers that alternate in orientation and have (1,4) glycosidic linkages (bundle of ~80 cellulose molecules)
Define glycogen and describe its structure. (Solubility, function, type of monomer, structure)
Water-soluble polymer of alpha-glucose that is used in animal storage; all alpha-glucose monomers are orientated in the same direction and have (1,4) glycosidic linkages; branched
What is the composition of a nucleotide?
Pentose, nitrogenous base, and 1+ phosphate groups
One 6-membered ring of carbon and nitrogen atoms (includes cytosine, thymine, and uracil)
Larger than pyrimidines; made up of a 6-membered ring fused to a 5-membered ring (includes adenine and guanine)
What is the sugar-phosphate backbone, and how is it formed?
Repeating pattern of sugar-phosphate units joined by phosphodiester bonds (phosphate linking two sugars)
In DNA/RNA, describe the linkage between the pentose and the nitrogenous base.
1'C covalently bonds to the bottom N (N opposite the double bond in pyrimidines, N not double-bonded in purines)
In DNA/RNA, which bases pair?
Adenine and Thymine (or Uracil)
Cytosine and Guanine
How is double-stranded DNA held together?
Through the hydrogen bonds between complementary nitrogenous bases
How can RNA become double-stranded?
RNA can form "stems" and "loops" in which its nitrogenous bases form complementary hydrogen bonding; this characteristic leads to complex structures that look like proteins
What is the basic structure of an amino acid? What is the "amino" part and what is the "acid" part?
Amino- refers to amino group
Acid- refers to carboxyl group (with the H)
Which amino acids contain chiral carbons?
All of the amino acids except for glycine.
What determines polarity of the R group? What determines if an R group is acidic or basic?
Presence of only methyl groups (non-polar) vs presence of hydroxyl groups (polar).
Carboxyl group-> Acidic
Amino group-> Basic
Describe x-ray crystallography.
X-ray beam is shot at crystallized protein, and the digital detector shows an X-ray diffraction pattern, which can be decoded by computation.
How is the secondary structure of protein formed at the molecular level?
Hydrogen bonds form between units of the peptide backbone (b/w the amino and O from carboxyl groups)
How is the tertiary structure of proteins formed at the molecular level?
Different bonds (covalent, ionic, hydrogen, van der waals) between the R-groups
What disease occurs when the 6th amino acid for the beta subunit of hemoglobin is replace with Valine?
What is the composition and function of a fat?
Glycerol + 3 fatty acids
What is the composition and function of a phospholipid?
Glycerol + 2 fatty acids + phosphatidyl choline (phosphate group + choline)
Used in structure of membranes
Draw glycerol. Does it have any asymmetric carbons?
Draw a fatty acid.
Having both hydrophobic and hydrophilic parts.
Why are saturated fats solid at room temperature, and unsaturated fats liquid?
Having only saturated fatty acids allows them to pack more tightly; having double bonds disrupts this structure
What polarity of molecules can most easily pass through the phospholipid membrane?
Diffusion down a concentration gradient
Can proteins diffuse "in" the membrane?
Yes. Fusing two cell membranes with different integral proteins will turn into a large cell membrane with equally diffused different proteins.
What factors affect membrane diffusion rates?
Temperature (low-> low rate), saturation state in fatty acids (lots of unsaturated fatty acids-> low rate), amount of cholesterol (moderate temp-> low rate; low temp-> higher rate)
What are the three ways of membrane transport?
Facilitated diffusion, active transport, bulk transport
Describe the two mechanisms of facilitated diffusion.
Channel protein- specific for certain ions
Carrier protein- ligand changes conformation and can transport many different ions
Describe an example of active transport. Does this require ATP?
The sodium-potassium pump pumps ions up the concentration gradient. This requires ATP.
Name the two ways of bulk transport.
Endocytosis and exocytosis
When a vesicle fuses with the plasma membrane to release a large amount of molecules.
When a vesicle buds from the membrane to bring a large amount of molecules in the cell.
What are the differences between prokaryotes and eukaryotes?
Eukaryotes are larger and have membrane-bound organelles.
What are the differences between animal and plant cells?
Animal cells have centrioles and intermediate filaments. Plant cells have cell walls, chloroplasts, and central vacuoles.
What is the technique used to separate different components of the cell?
Describe the process of making a protein-specific antibody (mouse experiment).
1. Protein is injected in mouse/animal.
2. Mouse produces lots of protein-specific antibodies.
3. Mouse's blood/serum is collected.
4. Fluorescent protein (like GFP) is attached to antibodies.
5. Put GFP antibodies on dead cells with tiny holes in the membrane.
In the making a protein-specific antibody (mouse) experiment, why must the cells be killed to place antibodies on them?
The antibodies cannot go through the cell membrane, so tiny holes must be made, and consequently end up killing the cell.
Describe the process of directly fusing the protein with a fluorescent protein. What is the benefit of this approach?
1. Add fluorescent protein (GFP) to DNA.
2. Transcribed RNA also has GFP.
3. End product protein has tagged GFP.
Movement of protein in the cell can be observed as the cells are still alive.
What is the structure and function of the nucleus?
Structure- outside membrane is contiguous with rough ER
Function- contains genetic material, DNA replication, transcription of mRNAs, transport of mRNAs to cytoplasm, assembly of ribosomes
What is the function of the nucleolus?
Region of the nucleus that creates ribosomal RNA
What is the structure and function of the rough ER?
What is the structure and function of the smooth ER?
Lipid synthesis (vesicles bud off and fuse into cell membrane), detoxification, and calcium ion storage
What is the structure and function of a ribosome? What is it made up of?
Machine of protein synthesis
Two subunits, made out of proteins and rRNA
What is the structure and function of the Golgi apparatus?
Acts as a "post office." Receives proteins at the cis face, sends proteins at the trans face.
Protein modification, polysaccharide formation, protein sorting into vesicles
What is the structure and function of a lysosome?
Acidic organelles that contain digestive enzymes
Phagocytosis (digesting food), autophagy (digesting damaged cell parts)
What is the structure and function of mitochondria?
Double membrane & has its own DNA
What are the differences between bound and free ribosomes?
Free ribosomes produce proteins that remain in the cytoplasm. Ribosomes bound to the ER produce membrane proteins or secreted proteins, and move these to the ER lumen.
What is the structure and function of a chloroplast?
Produces energy by using light
What is the structure and function of microtubules? What structures do they form? Are they present in animal/plant cells?
Structure- constantly changing tubes made out of tubulin dimers
Function- act as tracks for motor proteins
Form centrioles, cilia, flagella
Present in both animal and plant cells
What is the structure and function of intermediate filaments? Are they present in animal/plant cells?
Structure- very stable filaments made out of monomers
Function- maintain cell shape
Present only in animal cells
What is the structure and function of microfilaments? Are they present in animal/plant cells?
Structure- constantly changing filaments made out of actin
Function- act as tracks for motor proteins
Present in both animal and plant cells
What are the three main hypotheses for life? Describe them.
Early organics were made from radiation and lighting on inorganic molecules.
Alkaline hydrothermal vents provided the high pH and warm temperatures conducive for life.
Meteor provided organic molecules
Describe the Miller-Urey experiment.
Take the inorganic molecules that made up earth's early atmosphere, and run them through simulation "radiation and lightning". Results showed that some organic molecules WERE formed.
Name the different cell junctions in animal and plant cells.
Animal cells have gap junctions.
Plant cells have plasmodesmata.
Describe the embryo dissociation and reaggregation experiment. What is the reason for the results?
Mixing single cells together and allowing them to separate shows that cells of one type stick together. This self organization is due to proteins on the cell surface.
Describe the mesoderm induction experiment. Where are the secreting cells and where are the receiving cells?
When the mesoderm of a frog blastula is removed, the endoderm secretes signals to the ectoderm so they turn into mesoderm cells. Endoderm is secreting and ectoderm is receiving.
Describe the vulva induction experiment. How do the results tell us which cells make/receive the signal?
Without a vulva, the c. elegans worm will die due to being unable to release its eggs. Therefore, by getting rid of certain cells and observing the worm's eventual phenotype, we can tell which cells make or receive the signal.
How are signal proteins secreted within the cell?
Signal proteins first bud off the rough ER, then are shipped to the Golgi, then vesicles bud off and fuse with the cell membrane alike to exocytosis.
How are signal proteins received by a cell?
What are the three kinds of membrane-bound receptors?
G-protein coupled receptors, receptor tyrosine kinases, and gated ion channel receptors
Describe the activation of a G protein coupled receptor.
Describe the activation of a receptor tyrosine kinase.
Describe how ligand gated ion channel receptors work.
What is a phosphorylation cascade?
Sometimes when the receptor tyrosine kinase is activated, it begins a phosphorylation cascade in which the phosphate group is repeatedly passed through different molecules, until it eventually reaches the nucleus.
What is the structure of cyclic AMP?
What is the role of cyclic AMP as a secondary messenger?
When the activated adenylyl cyclase sends a signal to cAMP, cAMP releases a signal
How do steroid hormones travel through the body to reach target cells?
Endocrine cell releases hormones into bloodstream, which then go through the cell membrane to meet the target receptor in the cytoplasm.
Describe the pathway for XY chromosome leading to formation of testes.
XY chromosome-> SRY protein-> testosterone-> testes
XX chromosome-> no SRY protein-> no testosterone-> ovaries
What is the function of epinephrine?
Amplification of cell signal (production of many secondary messengers in transduction).
What is the function of ATP and GTP in cell signaling?
Release of energy and phosphorylation
What is the difference between substrate-level vs "bulk" phosphorylation of ADP?
Substrate level- phosphorylation of individual ADPs by enzymes, occurs in glycolysis and TCA cycle
Bulk- occurs in oxidative phosphorylation with ATP synthase
Describe the "electron route" during cellular respiration.
glucose-> NADH-> ETC-> oxygen
Summarize the inputs and outputs in glycolysis (in order).
Glucose -(2 ATP to ADP)-> 2 3-carbon molecules
(1 NAD+ reduced to NADH, 2 total)
(2 ADP phosphorylated to ATP, 4 total)
TOTAL PER GLUCOSE: 2NADH + 2 ATP
Summarize the inputs/outputs in the linking step of pyruvate oxidation.
(Carboxyl functional group-> CO2), later diffuses out of cell
(Coenzyme A is attached to remaining molecule)
Summarize the inputs/outputs in TCA cycle.
Acetyl CoA + oxaloacetate
(input and output of water)
(NAD+-> NADH) (removal of CO2)
(NAD+-> NADH) (removal of CO2)
(input of water)
TOTAL PER ACETYL COA: 3NADH + ATP + FADH2
Summarize the electron transport chain.
What is a major regulatory point in cellular respiration?
Negatively regulated by ATP and citrate
Positively regulated by AMP
Are PSII and PSI equally present in the granum?
No. PSI are usually outside of the granum, which PSII is present in the granum.
Describe the light reactions in photosynthesis.
Describe the Calvin cycle.
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